Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Bottom Line:
Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Mentions:
To explore the evolutionary process of chickpea F-box genes, we analyzed the comparative synteny maps between chickpea and M. truncatula, G. max, L. japonicus and Arabidopsis genomes. Amongst the legume species, maximum synteny was found between chickpea and soybean where 106 F-box genes from chickpea shared synteny with 335 F-box genes from soybean (Figure 5A). In contrast 112 chickpea F-box genes were syntenic with 148 F-box genes from M. truncatula (Figure 5B). Chickpea and L. japonicus were found to have the fewer genes in common with only 94 of the chickpea F-box genes having 127 corresponding orthologs in L. japonicus (Figure 5C). On the other hand, only 24 chickpea F-box genes showed synteny with 38 Arabidopsis F-box genes (Figure 5D).Figure 5

Mentions:
To explore the evolutionary process of chickpea F-box genes, we analyzed the comparative synteny maps between chickpea and M. truncatula, G. max, L. japonicus and Arabidopsis genomes. Amongst the legume species, maximum synteny was found between chickpea and soybean where 106 F-box genes from chickpea shared synteny with 335 F-box genes from soybean (Figure 5A). In contrast 112 chickpea F-box genes were syntenic with 148 F-box genes from M. truncatula (Figure 5B). Chickpea and L. japonicus were found to have the fewer genes in common with only 94 of the chickpea F-box genes having 127 corresponding orthologs in L. japonicus (Figure 5C). On the other hand, only 24 chickpea F-box genes showed synteny with 38 Arabidopsis F-box genes (Figure 5D).Figure 5

Bottom Line:
Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.